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Evolution Paper Topics

 * 1) Eocyte Hypothesis
 * 2) Homoplasy
 * 3) Clonal Interference
 * 4) Punctuated Gradualism
 * 5) Semantides

Citation Exercise
The classification of crocodiles known as gharials are made up of two different species: Gavialis gangeticus and Tomistoma schlegelii.

Homoplasy, in biology and phylogenetics, is when a trait has been gained or lost independently in separate lineages over the course of evolution. This is different from homology, which is the similarity of traits due to common ancestry. Homoplasy can arise from both similar selection pressures acting on adapting species, and the effects of genetic drift.

Most often, homoplasy is viewed as a similarity in morphological traits. However, homoplasy may also appear in other trait types, such as similarity in the genetic sequence, life cycle types or even behavioral traits.

Etymology
The term homoplasy was first used by Ray Lankester in 1870. The corresponding adjective is either homoplasic or homoplastic. It is derived from the two ancient greek words, meaning "similar, alike, the same", and  , meaning "to shape, to mold".

Parallelism and convergence
Parallel and convergent evolution lead to homoplasy when different species independently evolve or gain a comparable trait, which diverges from the trait inferred to have been present in their common ancestor. When the similar traits are caused by an equivalent developmental mechanism, the process is referred to as parallel evolution. The process is called convergent evolution when the similarity arises from different developmental mechanisms. These types of homoplasy may occur when different lineages live in comparable ecological niches that require similar adaptations for an increase in fitness. An interesting example is that of the marsupial moles (Notoryctidae), golden moles (Chrysochloridae) and northern moles (Talpidae). These are mammals from different geographical regions and lineages, and have all independently evolved very similar burrowing characteristics (such as a cone-shaped heads and flat frontal claws) to live in a subterranean ecological niche.

Reversion
In contrast, reversal (a.k.a. vestigialization) leads to homoplasy through the disappearance of previously gained traits. This process may result from changes in the environment in which certain gained traits are no longer relevant, or have even become costly. This can be observed in subterranean and cave-dwelling animals by their loss of sight, in cave-dwelling animals through their loss of pigmentation , and in both snakes and legless lizards through their loss of limbs.

Distinguishing homology from homoplasy
Homoplasy, especially the type that occurs in more closely related phylogenetic groups, can make phylogenetic analysis more challenging. Phylogenetic trees are created by means of parsimony analysis. These analyses can be done with phenotypic, as well as genetic traits (DNA sequences). Using parsimony analysis, the hypothesis that requires the fewest evolutionary changes is preferred over alternative hypotheses. Construction of these trees may become a challenge when clouded by the occurrence of homoplasy in the traits used for the analysis. The most important approach in overcoming these challenges, is by increasing the amount of independent (non-pleiotropic, non-linked) characteristics used in the construction of these phylogenic trees. Along with parsimony analysis, one could perform a likelihood analysis, where the probability of a tree being true is calculated and branch lengths are measured; and bootstrapping, in which trees are constructed for each characteristic separately to estimate the confidence of a tree.

According to cladistic interpretation, homoplasy can be identified when a given similarity in trait cannot be explained by relation through a common ancestor on a preferred phylogenetic hypothesis - that is, the feature in question arises (or disappears) at more than one point on the tree.

In the case of DNA sequences, homoplasy cannot be avoided due to its four-state nature. An observed homoplasy may simply be the result of random nucleotide substitutions accumulating over time, and thus may not need an adaptationist evolutionary explanation.

Real world examples and applications of homoplasy
Tarantula morphology tends to be excessively homoplastic, which has led to many misidentifications in their phylogenetic analysis. Ortiz, Francke, and Bond conducted a study on the genus Bonnetina, whose members exhibited remarkable heterogeneity to the point that their monophyly was questioned. Additionally, previous attempts at pinpointing the phylogenetic position of Bonnetina were arguably unsuccessful. Their study aimed to address these two issues, as well as create a timeline in the evolution of Bonnetina, and determine the reliability of tarantula classification based on morphology. Due to known issues with homoplasy among tarantulas, they planned to tackle these issues with a molecular approach. They sampled DNA from numerous taxa, and created five nuclear markers and one mitochondrial marker to sequence the genes of interest. The data were analyzed using several different models, such as maximum likelihood estimates and Bayesian methods. As a result of their study, they concluded that Bonnetina was indeed monophyletic, with the exception of Bonnetina juxtantricola. The last common ancestor of all tarantulas was about 92 million years ago, with Bonnetina diverging from its sister taxa about 19 million years ago. Most importantly, they confirmed that nearly all morphological traits within the genus Bonnetina were homoplastic. Only sexual features were observed to not be homoplastic, suggesting that sexual selection may have been a driving force in the divergence of tarantulas.

The phylogeny of gharials, a classification of crocodiles, is also significantly impacted by homoplasy. These endangered reptiles are made up of two different species: Gavialis gangeticus and Tomistoma schlegelii. An important distinction between the two is that under morphological analysis of extant species and fossils, Tomistoma is considered a true crocodile, while Gavialis is not, with the two species' shared characteristic of fish eating being a product of homoplasy. However, molecular data suggests that the gharials are sister taxa, with their shared fish eating trait being a result of homology. Further complicating matters is molecular and morphological data suggesting that the genus of thoracosaurs emerged within the lineage of gharials, despite the fact that the now extinct thoracosaurs actually emerged much sooner than gharials. Lee and Yates conducted a study aiming to combine molecular and morphological methods in order to address this anomaly and distinguish which traits were due to homology, and which were due to homoplasy. They checked living and fossilized crocodiles for a comprehensive list of known traits, and created a supermatrix made up of 10 nuclear genes. The resulting data were analyzed by parsimony and tip dating methods. From their research, they confirmed that the two species of gharials were indeed sister taxa, meaning that the shared traits between Tomistoma and true crocodiles were a result of homoplasy. They also concluded that the only possible explanation for the data placing thoracosaurs within the gharial lineage was a significant amount of homoplastic convergence between thoracosaurs and Gavialis. .

There are numerous other documented examples of homoplasy within evolutionary systems, such as within Eusiroidea (Crustaceans and Amphipoda), Urticaceae , Asteraceae , Polypodioideae (Selligueoid Ferns) , Ants , and Merluccius capensis (Cape Hakes).

The occurrence of homoplasy can also be used to make predictions about evolution. Recent studies have used homoplasy to predict the possibility and the path of extraterrestrial evolution. For example, Levin et al. (2017) suggest that the development of eye-like structures is highly likely, due to its numerous, independently evolved incidences on earth.

Homoplasy vs. evolutionary contingency
In his book Wonderful Life, Stephen Jay Gould claims that repeating the evolutionary process, from any point in time onward, would not produce the same results. The occurrence of homoplasy is viewed by some biologists as an argument against Gould’s theory of evolutionary contingency. Powell & Mariscal (2015) argue that this disagreement is caused by an equivocation and that both the theory of contingency as well as homoplastic occurrence can be true at the same time.